.\" Process this file with
.\" groff -man -Tascii foo.1
.\"
.TH DPOCKET 1 "JANUARY 2009" Linux "User Manuals"
.SH NAME
dpocket \- calculate descriptors on protein pockets.
.SH SYNOPSIS
.B dpocket -f
.I pdb-list
.B [OPTIONS]
.SH DESCRIPTION
.B dpocket 
is a program written to calculate descriptors on protein pockets.
It takes as basic input a file containing a list pf pdb file
name/path, with an associated ligand represented by its resname
in the pdb ( 3letter code). Both should be separated by a tabulation.

.I PATH/1BXO.pdb    GTD

.I PATH/1BBC.pdb    GTE

.I ...

Three file are created as output. One contains all pockets explicitely
defined using one of the two methods available for this explicit definition.
The two others contains all pockets as found by fpocket algorithm. One contain
all pockets that match either the overlap or the distance criteria, and the
other contains all pockets that does not match any of these criteria.

See the documentation for more details on output, methods, and on descriprots
currently availables.

.SH OPTIONS SPECIFIC TO DPOCKET

.IP -o
.I dout_file
.B [string]

Prefix of the output files. Otherwise, output files are writen
in the current directory, having the default prefix.

.B DEFAULT: dpout

.IP -e
.B [no value needed]

Use the first explicit interface definition (default): we define the
explicit pocket as being all atoms contacted by alpha spheres situated
at a distance of d A° from any ligand atom.

.B DEFAULT: used

.IP -E
.B [no value needed]

Use the second explicit interface definition: we define the
explicit pocket as being all atoms situated
at a distance of d A° from any ligand atom.

.B DEFAULT: not used

.IP -d
.I dist
.B [float]

Distance used by the explicit pocket definition.

.B DEFAULT: 4.0

.SH OPTIONS SPECIFIC TO FPOCKET

.B Use man fpocket.

.SH BUGS
.SH AUTHOR
.BR Developpers:

Peter Schmidtke <pschmidtke@mmb.pcb.ub.es>

Vincent Le Guilloux <vincent.le-guilloux@univ-orleans.fr>

.BR Supervisor:

Pierre Tuffery

.SH "SEE ALSO"
.BR fpocket (1),
.BR tpocket (1),


